Death brings out her timer and a shadow of Unity appeared and she says "I thought I was dead." Death's reply is: THIS IS ONLY THE BEGINNING - Does this mean we are going to see Unity in again?

No. She's dead.

On a completely different topic, one which nobody has ever mentioned either here [or] on CA.

Am I right in assuming it's the same storm and lightning bolt in ToT as in Nightwatch, which sends Vimes and Carcer back in time?

Yep. Unity's definitely dead and, as Death says, about to start her afterlife which, for her, should be a doddle presuming she still has vestiges of her auditor life so she's able to handle disincarnation very easily... Or maybe ghosting isn't for her and she'll have a go at reincarnation?

Bringing us to another interesting aspect, since we don't see any other auditor getting met by Death (and surely, as they are his ultimate enemies, he would have been very busy with all of them before Unity arrived in the desert). Does this mean that the other auditors, not having been incarnate for too long, and not having learned anything about living, therefore haven't developed the very thing (supposedly) that they may have actually understood about human physicality - the soul or spirit?

In turn, does that mean that the auditors are in fact souls in their natural state and so cannot be taken by death as they're still the same entities merely clothed in hastily assembled flesh? Unity, having tried very hard to immerse herself into being human (and not having any other auditor around to infuriate or fight with her) has had the time to 'get' what's being human means. That's done in a limited way since she's picking up on all the sensate positives and so has investigated the aspects that appeal to her most, becoming a kind of analytical aesthete (instead of an analytical psychopath) and is impressed and wanting to know more so she does acquire a human-like soul that Death can take...

Interesting point about the storm with Vimes and Carcer Pooh, but didn't that happen at night? It would be a great twist if it was the same storm though

"Some men see things as they are and ask why. Others dream things that never were and ask why not.” George Bernard Shaw

I certainly agree that it's the same storm in Thief of Time and Nightwatch, although whether Terry had the idea for Nightwatch at the time of writing ToT or not we may never know.

As to Unity - she'd gained enough humanity to deserve a soul and I think I'd agree with that. It was also rather a nice way to end her part in the story as I think, as she admits, that for her to stay alive would have driven her crazy. Humanity takes a lifetime to get used to.

“Men never commit evil so fully and joyfully as when they do it for religious convictions.” – Blaise Pascal

I would agree with that. I'd thought that the lightning in Night Watch hit the University, but aparently it didn't:

Night Watch wrote: “Mister Vimes?” “What?” Vimes snapped. Smoke was rising from the weathercock's bearings. “I got three knives, Mister Vimes,” said Carcer, bringing his arm up. The lightning struck. Windows blew out and iron gutters melted. Roofs lifted into the air and settled again. Buildings shook. But this storm had been blowing in from far across the plains, pushing the natural background magic ahead of it. It dumped it now, all in one go.They said afterwards that the bolt of lightning hit a clock-maker's shop in the Street of Cunning Artificers, stopping all the clocks at that instant. But that was nothing. In Baker Street a couple who had never met before became electrically attracted to one another and were forced to get married after two days for the sake of public decency. In the Assassins' Guild, the chief armourer became hugely, and since he was in the armoury at the time, tragically attractive to metal. Eggs fried in their baskets, apples roasted on the greengrocers' shelves. Candles lit themselves. Cartwheels exploded. And the ornate tin bath of the Archchancellor of Unseen University was lifted neatly off the floor, sizzled across his study and then flew off the balcony and on to the lawn in the octangle several storeys below, without spilling more than a cupful of suds.

Not me on either count normally Dotsie! Well perhaps the mouthie bit but only when I'm really pushed, and he does... He's fantasising about day-glo paint (and possibly PVC raincoats) again - odds on he's been sniffing it too (the paint)

With Susan it's rather touching to have kindergarten/infant school evoked for people of a certain age - the stationery cupboard and the milk & straw monitors - I lurved pricking the milk tops with the double-pointed sky-blue knitting needle - god knows what bacterial delights lurked on that 'cos it was never washed to my knowledge and then holding the jar of straws as everyone queued for their quarter pint bottle ( a very quiet and polite queue of course - we had a nun hovering the whole time... ). And there was always a kid like Jason and someone who leaked at the slightest provocation (and got the manky ancient navy-blue cotton knickers to wear for the rest of day...

We didn't have such brilliant field trips - if we were lucky that was a quick trip across the road to have 'games' in the park that was handily around the corner. We did have a class radio though with 'proper' actors for William the Conqueror or Richard the Lionheart when we had History and a singing lesson that was cosily and traditionally folksy that we could sing along with. Not being allowed to listen to the radio was a much worse punishment than the ruler or standing in the corner - they were genius at torturing kids were nuns...

"Some men see things as they are and ask why. Others dream things that never were and ask why not.” George Bernard Shaw